RetrogeneDB ID: retro_ttru_1603

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_55808:303..980(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSTTRG00000002459
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_ttru_1603
GAAAAAATAGCCCAGTTTGATGTTAAAAAGTTTGCAGAGAACCAGCCTAAAAGGACACCCCATGGAAAGAGAAAGTTTCT
TGAGAAGAGAAGAAGAAGCCCCAAGCTGAGCGGAAGGAGAAGAAGACAGCTGCCTCTGCTACTGAGGAGGCGCTGGATGA
ATGTGAGCAGGCATTGGCTGCTGAGCAGAAGGCCAAGGATCCCTTTGCTCACCTGCCCAAGAGTAACTTTGTGTTGGATG
AATTTAAGCGCAAGTACTCCAACGAGGACACACTCTCCGTGGTGCTGCCGTACTTTTGGGAGCACTTTGATAAAAATGGC
TGATTCCTGTGGTACTGCAACTACTGCTTCCCTGAAGAGCTCACCCAGACATTCATAAGCTGCAACCTTATCAATGGAAT
GTTCCAGCAATTGGACAAACTGAGGAAGAATGCCTTTGCCAGTGTCATTCTATTTGGAACCAACAATAGCAGCTCCATTT
CTGGAGTCTGAGTCTTCCGAGACCAGGAACTTGCCTTTCCCCTGAGTCCAGATTGGCAGGTGGATTATGAGTCATACACA
TAGCAGAAACTGGATCCCAGCAGCAAGGATATCCAGCCACTGGTTCAAGAATATTTTTCCTGGGATGGGGTCTTCCAGCA
TGCGGGCAAAGCCTTTAATCAGGGCAAGATCTTCAAG

Alignment

ORF - retro_ttru_1603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 52.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKMAQFDAKKFAESQPK-KDTPRKEKASREEKQKPQAERKEEKKAAAPAPEEELDECEQALAAEPKAKDP
          EK.AQFD.KKFAE.QPK.KDTP.KEK.S.EEK.KPQAERKE.KK.AA.A.EE.LDECEQALAAE.KAKDP
Retrocopy EKIAQFDVKKFAENQPK<KDTPWKEKVS*EEKKKPQAERKE-KKTAASATEEALDECEQALAAEQKAKDP

Parental  FAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRL
          FAHLPKS.FVLDEFKRKYSNEDTLSV.LPYFWEHFDK.G..LWY..Y.FPEELTQTF.SCNLI.GMFQ.L
Retrocopy FAHLPKSNFVLDEFKRKYSNEDTLSVVLPYFWEHFDKNG*FLWYCNYCFPEELTQTFISCNLINGMFQQL

Parental  DKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPSSEETQTLVREYFSW
          DKLRKNAFASVILFGTNNSSSISGV.VFR.QELAFPLSPDWQVDYESYT..KLDPSS...Q.LV.EYFSW
Retrocopy DKLRKNAFASVILFGTNNSSSISGV*VFRDQELAFPLSPDWQVDYESYT*QKLDPSSKDIQPLVQEYFSW

Parental  DGAFQHVGKAFNQGKIFK
          DG.FQH.GKAFNQGKIFK
Retrocopy DGVFQHAGKAFNQGKIFK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1603 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1603 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011843	1 retrocopy	retro_btau_1600,
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Myotis lucifugus	ENSMLUG00000000342	1 retrocopy	retro_mluc_1110,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Otolemur garnettii	ENSOGAG00000000827	1 retrocopy	retro_ogar_1344,
Ochotona princeps	ENSOPRG00000014563	1 retrocopy	retro_opri_814,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Pteropus vampyrus	ENSPVAG00000003440	1 retrocopy	retro_pvam_1239,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sus scrofa	ENSSSCG00000013064	1 retrocopy	retro_sscr_164,
Tursiops truncatus	ENSTTRG00000002459	3 retrocopies	retro_ttru_1082, retro_ttru_1544, retro_ttru_1603 ,